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  <title>BtToxin_scanner2 User Guide</title>
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 <p><strong>BtToxin_scanner2 (v1.0) </strong></p>
 <p><strong>Description </strong></p>
 <p> &nbsp; &nbsp;BtToxin_scanner2 is a high-throughput tool to extract Bt toxins from next-generation sequencing datas. The pipeline include several steps for processing the sequence data. Step 1, Abyss is used for genome assembly from pair-end reads. Step 2, Coding sequences (CDS) are predicted by Prodigal. Step 3, the putative target protein genes are mined.</p>
 <p><p>
 <p><strong> Requirements </strong></p>
 <p><ul><li><a href="http://www.bcgsc.ca/platform/bioinfo/software/abyss" title="ABySS" target="_blank">&nbsp;ABySS</a></p>
 <p><li><a href="http://compbio.ornl.gov/prodigal/" title="Prodigal" target="_blank">&nbsp;Prodigal</a></p>
 <p><li><a href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/" title="BLAST+" target="_blank">&nbsp;BLAST+</a></p>
 <p><li><a href="http://www.gnu.org/software/parallel/" title="GNU Parallel" target="_blank">&nbsp;GNU Parallel</a></ul></p>
 <p>&nbsp;</p>
 <p><strong>Usage and example: </strong></p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;for reads: BtToxin_scanner2.pl -s reads -1 .R1.clean.fastq.gz -2 .R2.clean.fastq.gz </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;for contigs/scaffolds: BtToxin_scanner2.pl -s assembled -3 "-8.fa"</p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;for CDs: BtToxin_scanner2.pl -s cds -p CDs -4 ".faa" -5 ".ffn" </p>
 <p><strong>Essential: </strong></p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The suffix name of reads 1 (for example: if the name of reads 1 is "YBT-1520_L1_I050.R1.clean.fastq.gz", "YBT-1520" is the strain same, so the suffix name should be ".R1.clean.fastq.gz") </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-2 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The suffix name of reads 2(for example: if the name of reads 2 is "YBT-1520_2.fq", the suffix name should be _2.fq") </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-3 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The suffix name of contigs or scaffolds(default -8.fa) -s Input type for analysis(3 choices: reads, assembled, cds. default is reads) </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-p &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The path of CDs contain both amino acid sequences and nucleotide sequences(default CDs)</p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-4 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The suffix name of files contain amino acid sequences(default .faa) </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-5 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The suffix name of files contain nucleotide sequences(default .ffn) </p>
 <p><strong>Options: </strong></p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-h &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Show help </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-k &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; k-mer size for genome assembly (default 81) </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-n &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; number of cpus to use (default 6) </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-e &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; evalue for blast against the Bt toxin database (default 1e-5) </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-c &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; the minimum size of blast coverage(default 50) </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-g &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Specify a translation table to use for prodigal (default 11) </p>
 <p> &nbsp; &nbsp; &nbsp; &nbsp;-d &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Database for blastp (default Bt_toxin)</p>
 <p>&nbsp;</p>
 <p><strong>OUTPUT FILES</strong></p>
 <p>1. If the input files are reads, there will generate four directories</p>
 <p><ul><li>assembly: &nbsp;The assembled files produced by Abyss</li></p>
 <p><li>CDs: &nbsp;The cds predicted by Prodigal</li></p>
 <p><li>cry: &nbsp;The predicted toxins</li></p>
 <p>&nbsp;&nbsp;&nbsp;&nbsp;--new_genes/New_genes_unique.table: &nbsp;The table of new toxins</p>
 <p>&nbsp;&nbsp;&nbsp;&nbsp;--new_genes/gene_scaf_seqs3.txt: &nbsp;The scaffolds of new toxins</p>
 <p>&nbsp;&nbsp;&nbsp;&nbsp;--old_genes/Old_genes.table: &nbsp;The table of new toxins</p>
 <p><li>scaf: &nbsp;Scaffolds or the inputed reads</li></ul></p>
 <p>2. If the input files are contigs/scaffolds, there will generate two directories</p>
 <p><ul><li>CDs: &nbsp;The cds predicted by Prodigal</li></p>
 <p><li>cry: &nbsp;The predicted toxins</li></ul></p>
 <p>3. If the input files are CDs, there will generate one directories</p>
 <p><ul><li>cry: &nbsp;The predicted toxins</li></ul></p>
 <p>&nbsp;</p>
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